Alignments for a candidate for thrB in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrB in Klebsiella michiganensis M5al

Align homoserine kinase; EC 2.7.1.39 (characterized)
to candidate BWI76_RS04250 BWI76_RS04250 homoserine kinase

Query= CharProtDB::CH_002113
         (310 letters)



>FitnessBrowser__Koxy:BWI76_RS04250
          Length = 309

 Score =  556 bits (1434), Expect = e-163
 Identities = 269/308 (87%), Positives = 291/308 (94%)

Query: 1   MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGRFADKLPSEP 60
           MVKVYAPASSANMSVGFDVLGAAVTPVDG LLGD V+VEAA +FSL N+GRFA KLP+ P
Sbjct: 1   MVKVYAPASSANMSVGFDVLGAAVTPVDGTLLGDNVSVEAAASFSLQNVGRFASKLPTAP 60

Query: 61  RENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLND 120
           +ENIVYQCWERFCQE+GK++PVAMTLEKNMPIGSGLGSSACSVVAAL+AMNE CGKPLN+
Sbjct: 61  QENIVYQCWERFCQEIGKKVPVAMTLEKNMPIGSGLGSSACSVVAALVAMNEFCGKPLNE 120

Query: 121 TRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWVLAYPGI 180
           +R+LALMGE+EGRISGSIHYDNVAPC+LGG+QLM+EEN IISQQ+P FDEWLWVLAYPGI
Sbjct: 121 SRMLALMGEMEGRISGSIHYDNVAPCYLGGIQLMLEENGIISQQIPSFDEWLWVLAYPGI 180

Query: 181 KVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQPELAAKLMKDVIAEPYRERLLP 240
           KVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQP+LAAKLMKDVIAEPYR +LLP
Sbjct: 181 KVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQPQLAAKLMKDVIAEPYRTKLLP 240

Query: 241 GFRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVADWLGKNYLQNQEGFVHICRL 300
           GF +ARQA  EIGA A GISGSGPTLFALCDKPETAQRVADWL  +YLQNQEGFVHICRL
Sbjct: 241 GFSEARQAAMEIGAQACGISGSGPTLFALCDKPETAQRVADWLATHYLQNQEGFVHICRL 300

Query: 301 DTAGARVL 308
           DTAGARV+
Sbjct: 301 DTAGARVV 308


Lambda     K      H
   0.321    0.136    0.412 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 421
Number of extensions: 9
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 310
Length of database: 309
Length adjustment: 27
Effective length of query: 283
Effective length of database: 282
Effective search space:    79806
Effective search space used:    79806
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate BWI76_RS04250 BWI76_RS04250 (homoserine kinase)
to HMM TIGR00191 (thrB: homoserine kinase (EC 2.7.1.39))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00191.hmm
# target sequence database:        /tmp/gapView.23095.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00191  [M=304]
Accession:   TIGR00191
Description: thrB: homoserine kinase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                               Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   8.6e-124  398.3   0.0   9.7e-124  398.1   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS04250  BWI76_RS04250 homoserine kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS04250  BWI76_RS04250 homoserine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.1   0.0  9.7e-124  9.7e-124       1     302 [.       2     308 ..       2     309 .] 0.99

  Alignments for each domain:
  == domain 1  score: 398.1 bits;  conditional E-value: 9.7e-124
                               TIGR00191   1 lkvkvPassANlgpGfDvlGlalslvlellvtedvaqeskdk.sleaegegvekipkesdkNliyqvakkv 70 
                                             +kv++PassAN+++GfDvlG+a+++v++ l++++v++e++ + sl+++g++++k+p+ +++N++yq+++++
  lcl|FitnessBrowser__Koxy:BWI76_RS04250   2 VKVYAPASSANMSVGFDVLGAAVTPVDGTLLGDNVSVEAAASfSLQNVGRFASKLPTAPQENIVYQCWERF 72 
                                             69*********************************99999999**************************** PP

                               TIGR00191  71 lkklgkrvkpvkltvekeiplgrGLGSSaaaivaaviaanelaglklskeelldlalllEg......HpDN 135
                                             +++ gk+  pv++t+ek++p+g+GLGSSa+++vaa++a+ne++g++l+++++l+l++++Eg      H+DN
  lcl|FitnessBrowser__Koxy:BWI76_RS04250  73 CQEIGKK-VPVAMTLEKNMPIGSGLGSSACSVVAALVAMNEFCGKPLNESRMLALMGEMEGrisgsiHYDN 142
                                             *******.9************************************************************** PP

                               TIGR00191 136 vapallGGlqlavkeddllevlkvPsgsklkvvlviPnievsTaeaRavLPkaysrqdlvfnlshlavlvt 206
                                             vap++lGG+ql+++e+  ++++++Ps++++ +vl++P+i+vsTaeaRa+LP++y+rqd++++++hla++++
  lcl|FitnessBrowser__Koxy:BWI76_RS04250 143 VAPCYLGGIQLMLEENG-IISQQIPSFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGFIH 212
                                             *****************.***************************************************** PP

                               TIGR00191 207 AlvskdkadllaiamkDrvhqpyRekliPelteikqaakekgalgitlSGaGptilalaeeek.eekaqel 276
                                             A++s+ +++l+a++mkD++++pyR+kl+P+++e +qaa e ga + ++SG+Gpt++al+++ + +++++++
  lcl|FitnessBrowser__Koxy:BWI76_RS04250 213 ACYSR-QPQLAAKLMKDVIAEPYRTKLLPGFSEARQAAMEIGAQACGISGSGPTLFALCDKPEtAQRVADW 282
                                             *****.*********************************************************9******* PP

                               TIGR00191 277 leklakegieltvkvleldtdgaeve 302
                                             l +++ +++e++v++++ldt+ga+v+
  lcl|FitnessBrowser__Koxy:BWI76_RS04250 283 LATHYLQNQEGFVHICRLDTAGARVV 308
                                             ***********************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (309 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.33
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis